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THE UNIVERSITY OF HULL The influence of flow management and habitat improvement works on fish communities in Yorkshire rivers being a Thesis submitted for the Degree of Doctor of Philosophy in the University of Hull by Marie Jane Taylor BSc. (Hons) (Hull) MSc (Res) (Hull) May 2017 TABLE OF CONTENTS LIST OF TABLES V LIST OF FIGURES IX ACKNOWLEDGEMENTS XIII ABSTRACT XIV 1 GENERAL INTRODUCTION 1 2 IMPORTANCE OF THE NATURAL FLOW REGIME FOR FISH 5 Introduction 5 The natural flow regime 5 2.2.1 Timing 6 2.2.2 Continuity/predictability 7 2.2.3 Rapidity of change 7 2.2.4 Amplitude/ magnitude 8 2.2.5 Duration 9 Modification of natural flow regimes 9 2.3.1 Reservoirs 9 2.3.2 Flood Defence 11 Current UK guidance of flow regulation and flood risk management 14 River rehabilitation and mitigation measures with specific reference to reservoirs and flood defence 16 2.5.1 Reservoir mitigation measures 17 2.5.2 Biological responses to reservoir mitigation measures 21 2.5.3 Flood defence mitigation measures 22 2.5.4 Biological response to habitat improvement works whilst considering flood risk 25 Study species 27 3. INFLUENCE OF MODIFIED RESERVOIR FLOW RELEASES ON BROWN TROUT POPULATIONS IN DOWNSTREAM RIVER REACHES 29 3.1 Introduction 29 3.2 Methodology 33 3.2.1 Study area 33 3.2.2 Fish survey methodology 37 3.2.3 HABSCORE data collection 37 3.2.4 Data analysis 38 3.3 Results 43 3.3.1 Hydrological flow parameters 43 3.3.2 Brown trout population density trends 46 3.3.3 HABSCORE 53 3.4 Discussion 56 3.4.1 Overview 56 3.4.2 Hydrological trends 56 3.4.3 Brown trout population trends 57 3.4.4 Habitat trends 59 ii 3.5 Summary 60 4 INFLUENCE OF RESERVOIR FRESHET RELEASES ON INDIVIDUAL BROWN TROUT BEHAVIOUR 61 Introduction 61 Methodology 63 4.2.1 Study area 63 4.2.2 Sampling and tagging procedure 67 4.2.3 Radio tracking of brown trout 69 4.2.4 Missing brown trout / tag failure 69 4.2.5 Data analysis 71 4.2.6 Temperature 72 Results 72 4.3.1 Brown trout length 72 4.3.2 General movements 74 4.3.3 Influence of reservoir freshet releases on brown trout movements 88 4.3.4 Temperature profiles during freshet releases 92 Discussion 97 4.4.1 Overview 97 4.4.2 General movements and individual behaviours of brown trout 97 4.4.3 Influence of freshets on brown trout movement 98 4.4.4 Frequency of reservoir freshet releases 99 4.4.5 Duration of reservoir freshet releases 100 4.4.6 Magnitude of reservoir freshet releases 100 4.4.7 Rate of change of reservoir freshet releases 101 4.4.8 Timing of reservoir freshet releases 102 4.4.9 Water temperature 102 4.4.10 Habitat suitability 103 Summary 104 5 HABITAT IMPROVEMENT FOR FISHERIES IN RIVERS DOWNSTREAM OF RESERVOIRS IN YORKSHIRE 106 5.1 Introduction 106 5.2 Methodology 108 5.2.1 Study reaches 108 5.2.2 Fish survey methodology 113 5.2.3 HABSCORE data collection 114 5.2.4 Data analysis 115 5.3 Results 118 5.3.1 Ingbirchworth Dike and reference sites 118 5.3.2 River Washburn and reference sites 132 5.4 Discussion 147 5.4.1 Ingbirchworth Dike 147 5.4.2 River Washburn 149 5.4.3 Habitat improvement 151 5.5 Summary 153 6 BROWN TROUT RESPONSE TO HABITAT MODIFICATIONS AT MALIN BRIDGE 155 Introduction 155 Methodology 156 6.2.1 Study area 156 6.2.2 Fish survey methodology 157 iii 6.2.3 HABSCORE data collection 161 6.2.4 Data analysis 161 Results 162 6.3.1 Brown trout population density trends, Malin Bridge 2009 - 2014 162 6.3.2 Habitat overview 166 6.3.3 HABSCORE outputs 167 Discussion 170 Summary 174 7 GENERAL DISCUSSION AND RECOMENDATIONS 176 INTRODUCTION 176 7.1.1 The influence of flow on brown trout movements and key population parameters 176 7.1.2 The influence of habitat modifications on brown trout population parameters 178 7.1.3 The influence of freshets on temperature profiles 179 7.1.4 Management considerations when carrying out flow modifications and habitat improvement in rivers 179 CONCLUSIONS AND RECOMMENDATIONS 181 7.2.1 Reservoir flow release trials 181 7.2.2 Improving habitat for brown trout through river habitat improvement works 183 7.2.3 Water resource management (Future planning, prioritisation and climate change) 184 7.2.4 Study Design 184 Other factors influencing brown trout populations 185 Climate change 186 8 REFERENCES 188 9 APPENDIX 203 iv LIST OF TABLES Table 2.1. Impact of reservoirs on downstream ecosystems (modified from 13 Acreman et al., 2000 and Richter et al., 1998). Table 2.2. Ecological classes for waterbodies in the Water Framework 15 Directive (Taken and modified from Acreman & Ferguson, 2010). Table 2.3. Common habitat rehabilitation techniques to improve instream 23 channel habitats and processes (modified from Roni et al., 2013). Table 3.1. Original and revised flow release programme from Holme Styes, 35 Digley and Brownhill reservoirs into the rivers Holme and Ribble. Table 3.2. 0+ and >0+ brown trout abundance (N/100 m2) classifications 40 used in the Environment Agency Fisheries Classification Scheme (EA-FCS), colours are assigned for clarity in subsequent data analysis. Table 3.3. Densities (± 95% C.L at quantitative sites) of 0+ brown trout at 49 all sites in the rivers Holme and Ribble, 2002-2009 and 2012- 2013. Colours represent EA-FCS grading scheme. Table 3.4. Densities (± 95% C.L at quantitative sites) of >0+ brown trout at 50 all sites in the rivers Holme and Ribble, 2002-2009 and 2012- 2013. Colours represent EA-FCS grading scheme Table 3.5. Relationship between observed densities and those predicted 55 by HABSCORE HQS for 0+ trout, >0+ trout (<20 cm) and >0+ trout (>20 cm) in the rivers Holme and Ribble. Habitat data were divided into pre (2003 (2002 and 2003 fish density data)), short term post (2006 (2004- 2006 fish density data)) and long term post (2013 (2007-2009 and 2012 and 2013 fish density data)) flow change. +/- = density higher/lower than predicted. Shaded area represents sites where the observed population was significantly higher (blue) or lower (red) than would be expected under pristine conditions. NS denotes fish and HABSCORE not surveyed (Adapted from Bolland et al., 2011). Table 4.1. Number (n), date tagged and released, length (mean ± SD 70 (range), mm), mass (mean ± SD (range), g), ratio (%) of tag weight of brown trout, release location National Grid Reference (NGR) and number of tags failed/lost brown trout. Table 4.2. Definitions of terms used when analysing data. 71 Table 4.3. Range (mean ± SD (range), m) of individual brown trout in each 90 study reach during Brownhill Reservoir and Digley Reservoir freshet releases in October, November and December and a control day with no reservoir freshet release in 2012 and 2013. Shaded represents control data. Table 4.4. Total distance moved (mean ± SD (range), m) by brown trout in 90 each study reach during Brownhill Reservoir and Digley Reservoir freshet releases in October, November and December and a control day with no reservoir freshet release in 2012 and 2013. Shaded are represents control data. Table 4.5. UKTAG recommendations for autumn and winter flow elevations 99 to reach good ecological potential (UKTAG, 2013). Table 5.1. Fisheries survey site details for Ingbirchworth Dike habitat 114 improvement works (n/s = not sampled). Table 5.2. Fisheries survey site details for the River Washburn habitat 115 improvement works. v Table 5.3. 0+ and >0+ brown trout density (numbers of fish per 100m2) 120 and abundance classification at survey site locations for the Ingbirchworth Dike habitat improvement works (n/s = not sampled). Table 5.4. HABSCORE outputs for 0+ brown trout in Ingbirchworth Dike, 129 2014 habitat data incorporating fish data from annual surveys between 2012 and 2014. Shaded area represents sites where the observed population was significantly higher (HUI lower C.L. column; blue) or lower (HUI upper C.L. column; red) than would be expected under pristine conditions. Table 5.5. HABSCORE outputs for >0+ (<20 cm) brown trout in 129 Ingbirchworth Dike, 2014 habitat data incorporating fish data from annual surveys between 2012 and 2014. Shaded area represents sites where the observed population was significantly higher (HUI lower C.L. column; blue) or lower (HUI upper C.L. column; red) than would be expected under pristine conditions. Table 5.6. HABSCORE outputs for >0+ (>20 cm) brown trout in 130 Ingbirchworth Dike 2014, habitat data incorporating fish data from annual surveys between 2012 and 2014. Shaded area represents sites where the observed population was significantly higher (HUI lower C.L. column; blue) or lower (HUI upper C.L. column; red) than would be expected under pristine conditions. Table 5.7. HABSCORE outputs for 0+ brown trout in Ingbirchworth Dike 130 reference sites, 2014 habitat data incorporating fish data from annual surveys between 2012 and 2014. Shaded area represents sites where the observed population was significantly higher (HUI lower C.L. column; blue) or lower (HUI upper C.L. column; red) than would be expected under pristine conditions. Table 5.8. HABSCORE outputs for >0+ (<20 cm) brown trout in 131 Ingbirchworth Dike reference sites, 2014 habitat data incorporating fish data from annual surveys between 2012 and 2014. Shaded area represents sites where the observed population was significantly higher (HUI lower C.L.
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